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A youthful lad cries out as his skull is forcefully held, a massive thumb digging into his face as his parent's mighty palm holds him by the neck. That scene from The Sacrifice of Isaac appears in the Florentine museum, evoking distress through Caravaggio's chilling portrayal of the tormented youth from the scriptural account. The painting appears as if the patriarch, commanded by the Divine to kill his offspring, could break his spinal column with a single twist. Yet Abraham's preferred method involves the metallic steel knife he holds in his other palm, prepared to slit the boy's neck. A certain element stands out – whoever modeled as Isaac for this astonishing work demonstrated extraordinary expressive ability. There exists not only fear, surprise and begging in his shadowed gaze but additionally profound sorrow that a guardian could abandon him so completely.

The artist adopted a well-known scriptural story and transformed it so fresh and raw that its horrors seemed to unfold right in view of the viewer

Viewing in front of the painting, observers identify this as a actual countenance, an precise depiction of a young model, because the identical youth – identifiable by his disheveled locks and almost black pupils – features in two other paintings by Caravaggio. In each case, that highly emotional visage dominates the scene. In John the Baptist, he gazes mischievously from the shadows while holding a ram. In Amor Vincit Omnia, he grins with a hardness learned on Rome's alleys, his dark feathery appendages sinister, a naked child creating chaos in a well-to-do dwelling.

Victorious Cupid, presently displayed at a London museum, represents one of the most discomfiting artworks ever painted. Observers feel totally unsettled looking at it. Cupid, whose arrows fill people with frequently painful longing, is shown as a extremely real, brightly illuminated unclothed figure, standing over overturned objects that include musical instruments, a music score, plate armour and an builder's ruler. This heap of items resembles, deliberately, the mathematical and architectural equipment scattered across the ground in the German master's print Melancholy – save in this case, the melancholic disorder is created by this grinning deity and the turmoil he can release.

"Affection sees not with the vision, but with the mind, / And therefore is winged Cupid depicted blind," wrote the Bard, shortly prior to this painting was produced around 1601. But the painter's god is not blind. He gazes straight at you. That countenance – ironic and ruddy-cheeked, staring with brazen confidence as he struts unclothed – is the identical one that screams in fear in The Sacrifice of Isaac.

When Michelangelo Merisi da Caravaggio painted his three portrayals of the same distinctive-looking kid in the Eternal City at the dawn of the seventeenth century, he was the most celebrated sacred painter in a metropolis enflamed by Catholic revival. Abraham's Offering reveals why he was sought to decorate sanctuaries: he could adopt a biblical narrative that had been depicted many occasions previously and render it so fresh, so unfiltered and visceral that the terror appeared to be happening immediately in front of you.

However there existed another side to the artist, apparent as soon as he arrived in Rome in the cold season that concluded the sixteenth century, as a painter in his early 20s with no teacher or patron in the urban center, only talent and boldness. The majority of the works with which he captured the holy metropolis's attention were everything but holy. What could be the absolute earliest hangs in the UK's National Gallery. A young man opens his red lips in a yell of agony: while reaching out his filthy digits for a cherry, he has rather been bitten. Boy Bitten By a Lizard is sensuality amid poverty: viewers can see the painter's gloomy chamber reflected in the murky liquid of the transparent container.

The boy wears a rose-colored flower in his hair – a symbol of the sex commerce in early modern art. Northern Italian painters such as Titian and Palma Vecchio depicted prostitutes holding flowers and, in a painting destroyed in the second world war but documented through photographs, the master portrayed a renowned woman courtesan, clutching a bouquet to her bosom. The meaning of all these botanical signifiers is obvious: intimacy for purchase.

What are we to interpret of the artist's erotic depictions of youths – and of one adolescent in particular? It is a inquiry that has divided his interpreters ever since he gained mega-fame in the 1980s. The complex historical truth is that the painter was not the homosexual icon that, for instance, Derek Jarman presented on screen in his twentieth-century film Caravaggio, nor so entirely pious that, as certain artistic historians improbably assert, his Youth Holding Fruit is actually a likeness of Christ.

His early paintings indeed offer overt sexual implications, or including offers. It's as if the painter, then a destitute young creator, identified with Rome's sex workers, offering himself to live. In the Uffizi, with this idea in consideration, viewers might look to another early creation, the sixteenth-century masterwork Bacchus, in which the god of wine gazes coolly at the spectator as he begins to undo the dark ribbon of his garment.

A few annums after Bacchus, what could have driven Caravaggio to paint Victorious Cupid for the art collector the nobleman, when he was finally growing almost respectable with prestigious church projects? This profane pagan deity revives the sexual challenges of his initial paintings but in a increasingly intense, uneasy manner. Half a century later, its secret seemed clear: it was a representation of Caravaggio's lover. A English visitor viewed Victorious Cupid in about 1649 and was informed its figure has "the physique and countenance of [Caravaggio's|his] owne youth or assistant that slept with him". The name of this boy was Cecco.

The artist had been dead for about forty annums when this story was documented.